Natural Product: NPC70441

Natural Product IDNPC70441
Common Name
?
The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
(2S)-2-[2-[(2S,3R,4R,5S,6S)-3,5-Dihydroxy-6-Methyl-4-[(2S,3R,4S,5S,6R)-3,4,5-Trihydroxy-6-(Hydroxymethyl)Oxan-2-Yl]Oxyoxan-2-Yl]Oxy-5-Hydroxyphenyl]-5,7-Dihydroxy-2,3-Dihydrochromen-4-One
IUPAC Name (2S)-2-[2-[(2S,3R,4R,5S,6S)-3,5-dihydroxy-6-methyl-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyoxan-2-yl]oxy-5-hydroxyphenyl]-5,7-dihydroxy-2,3-dihydrochromen-4-one
Synonyms
Synthetic Gene Cluster n.a.
ChEMBL Identifier CHEMBL504524
PubChem CID 11995074
Chemical Classification
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000261] Phenylpropanoids and polyketides
      • [CHEMONTID:0000334] Flavonoids
        • [CHEMONTID:0000337] Flavans
          • [CHEMONTID:0001632] Flavanones

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

  Chemical Representations

Standard InCHIKey JTQOVBLCPLYXBN-VDBSBOKISA-N
Standard InCHI InChI=1S/C27H32O15/c1-9-20(33)25(42-26-23(36)22(35)21(34)18(8-28)41-26)24(37)27(38-9)40-15-3-2-10(29)4-12(15)16-7-14(32)19-13(31)5-11(30)6-17(19)39-16/h2-6,9,16,18,20-31,33-37H,7-8H2,1H3/t9-,16-,18+,20-,21+,22-,23+,24+,25+,26-,27-/m0/s1
SMILES C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)Oc1ccc(cc1[C@@H]1CC(=O)c2c(cc(cc2O1)O)O)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O

  Calculated Properties

Physi-Chem Properties

Molecular Weight:   596.17 Volume:   546.164
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Van der Waals volume.
Dense:   1.092 LogP:   0.387
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The logarithm of the n-octanol/water distribution coefficients.
logD7.4:   1.098
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The logarithm of the n-octanol/water distribution coefficient at pH=7.4.
LogS:   -2.66
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The logarithm of aqueous solubility value.
Rotatable Bonds:   6.0 Rigid Bonds:   30.0
TPSA:   245.29
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Topological Polar Surface Area.
H-Bond Acceptor:   15.0
H-Bond Donor:   9.0 Rings:   5.0
Heavy Atoms:   15.0

MedChem Properties

QED Drug-Likeness Score:   0.185 GASA:   0.0
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GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:   4.885 Fsp3:   0.519
MCE-18:   121.902
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MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.
Lipinski Rule-of-5:   Accepted
Pfizer Rule:   Rejected GSK Rule:   Accepted
Golden Triangle Rule:   Accepted BMS Rule:   1
Chelating Alert:   0 PAINS Alert:   0
Colloidal aggregators:   0.61 Fluc inhibitor:   0.507
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The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:   0.079
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The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1
Green fluorescence:   0.277
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The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:   0.211 Promiscuous compounds:   0.357

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:   -6.849 MDCK Permeability:   -4.972
Pgp-inhibitor:   0.0 Pgp-substrate:   0.254
PAMPA:   0.994
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The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).
Human Intestinal Absorption (HIA):   0.03
20% Bioavailability (F20%):   0.039 30% Bioavailability (F30%):   0.989
50% Bioavailability (F50%):   0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):   0.007 MRP1:   0.2
Plasma Protein Binding (PPB):   81.391% Volume Distribution (VD):   -0.161
Fu: 18.029%
?
The fraction unbound in plasms.
OATP1B1 inhibitor:   1.0
OATP1B3 inhibitor:   1.0 BCRP inhibitor:   0.274
BSEP inhibitor:   0.001

ADMET: Metabolism

CYP1A2-inhibitor:   0.008 CYP1A2-substrate:   0.0
CYP2C19-inhibitor:   0.0 CYP2C19-substrate:   0.16
CYP2C9-inhibitor:   0.0 CYP2C9-substrate:   0.0
CYP2D6-inhibitor:   0.0 CYP2D6-substrate:   0.262
CYP3A4-inhibitor:   0.0 CYP3A4-substrate:   0.239
CYP2B6-substrate:   0.0 CYP2C8-inhibitor:   0.816
HLM stability:   0.975
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Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):  1.896 Half-life (T1/2):  4.753

ADMET: Toxicity

hERG Blockers:  0.016 hERG Blockers (10um):  0.076
Human Hepatotoxicity (H-HT):  0.765 Drug-induced Liver Injury (DILI):  0.968
AMES Toxicity:  0.972 Rat Oral Acute Toxicity:  0.065
Maximum Recommended Daily Dose:  0.079 Skin Sensitization:  0.999
Carcinogencity:  0.14 Eye Corrosion:  0.0
Eye Irritation:  0.281 Respiratory Toxicity:  0.059
Drug-induced Neurotoxicity:  0.021 Ototoxicity:  0.98
Hematotoxicity:  0.173 Drug-induced Nephrotoxicity:  0.896
Genotoxicity:  0.979 RPMI-8226 Immunitoxicity:  0.292
A549 Cytotoxicity:  0.963 Hek293 Cytotoxicity:  0.86
BCF:   0.353
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Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].
IGC50:   2.939
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48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:   4.522
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48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].
LC50FM:   3.628
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96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

  Species Source

Organism ID Organism Name Taxonomy Level Family SuperKingdom Isolation Part Collection Location Collection Time Reference
NPO26960 Cyclosorus acuminatus Species Thelypteridaceae Eukaryota rhizomes n.a. n.a. PMID[17125239]
NPO26960 Cyclosorus acuminatus Species Thelypteridaceae Eukaryota n.a. n.a. n.a. Database[COCONUT]
NPO26960 Cyclosorus acuminatus Species Thelypteridaceae Eukaryota n.a. n.a. n.a. Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
UNPD: Universal Natural Products Database [PMID: 23638153].
StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
MetaboLights: a metabolomics database [PMID: 27010336].
FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



  NP Quantity Composition/Concentration

Organism ID Organism Name Organism Material Preparation Organism Part NP Quantity (Standard) NP Quantity (Minimum) NP Quantity (Maximum) Quantity Unit Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].



 Biological Activity

Molecular-level activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference

In vitro activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT1118 Organism Streptococcus pneumoniae Streptococcus pneumoniae MIC = 32.0 ug.mL-1 PMID[18426954]
NPT1122 Organism Haemophilus influenzae Haemophilus influenzae MIC = 32.0 ug.mL-1 PMID[18491868]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC = 128.0 ug.mL-1 PubChem BioAssay data set
NPT19 Organism Escherichia coli Escherichia coli MIC = 64.0 ug.mL-1 PubChem BioAssay data set

In vivo activity

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference





 Experimental ADME

Experiment Model Experiment Tissue ADME Type ADME Relation ADME Value ADME Unit Reference





 Experimental Toxicity

Quantitative toxicity

Experiment Model Experiment Organism Toxicity Type Toxicity Relation Toxicity Value Toxicity Unit Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption
Hepatotoxicity Carcinogenicity Mutagenicity Cardiotoxicity Respiratory Toxicity Eye Irritation Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]


  Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

●  The left chart: Distribution of similarity level between NPC70441 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.5 or Top200).

Similarity Score Similarity Level Natural Product ID
0.75 Intermediate Similarity NPC199079
0.6289 Remote Similarity NPC210808
0.596 Remote Similarity NPC288152
0.5814 Remote Similarity NPC26195
0.57 Remote Similarity NPC137871
0.5446 Remote Similarity NPC9002
0.5392 Remote Similarity NPC257011
0.5301 Remote Similarity NPC199335
0.5238 Remote Similarity NPC190217
0.52 Remote Similarity NPC472387
0.5119 Remote Similarity NPC477240
0.5056 Remote Similarity NPC160156
0.5056 Remote Similarity NPC92565
0.505 Remote Similarity NPC168789

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

●  The left chart: Distribution of similarity level between NPC70441 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
NPD

Bioactivity similarity

  Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
A: chemistry similarity;
B: biological targets similarity;
C: networks similarity;
D: cell-based bioactivity similarity;
E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity
B: biological targets similarity
C: networks similarity
D: cell-based bioactivity similarity
E: similarity based on clinical data